Trump CDC Changes: Vaccine Policy, Budget Cuts, and PEPFAR

Since President Trump began his second term in January 2025, changes at the CDC have touched almost every part of the agency: five people have run it in roughly 18 months, more than a quarter of the workforce is gone, the childhood vaccine schedule and the panel that sets it were rewritten and then partly reinstated by a federal judge, scientific publications and public data were paused or pulled down, and the agency’s role in global HIV work is being wound down. Several of the biggest Trump CDC changes have been blocked or narrowed in court, but the agency still has no Senate-confirmed director.

Who Is Running the CDC

The agency has cycled through acting and confirmed leaders since January 2025. Trump’s first nominee, former Republican congressman David Weldon, was withdrawn on March 13, 2025, after the White House concluded he lacked Republican votes; his hearing was canceled less than an hour before it was to begin.¹

Susan Monarez, a career public health official, was confirmed by the Senate in July 2025. Her tenure lasted about a month. On August 27, 2025, HHS announced she was “no longer director” after she refused directives from Health and Human Services Secretary Robert F. Kennedy Jr. to fire top CDC officials and accept specific vaccine recommendations from a panel Kennedy had stacked with vaccine skeptics.² Her attorneys said she had neither resigned nor been officially fired and had “refused to rubberstamp unscientific reckless directives.”³ Four senior career officials resigned in response, including the chief medical officer and the directors of two major disease centers.⁴

Kennedy then installed Jim O’Neill, the deputy health secretary, as acting director. O’Neill oversaw the January 2026 announcement of changes to the childhood vaccine schedule and departed in February 2026.⁵ Jay Bhattacharya, who also directs the National Institutes of Health, became acting CDC director in mid-February 2026. The Federal Vacancies Reform Act’s 210-day limit on acting service ran out on March 25, 2026, though he has continued performing the delegable duties of the position.⁶

On April 16, 2026, Trump nominated Dr. Erica Schwartz to be the permanent director. Schwartz is a retired rear admiral in the U.S. Public Health Service Commissioned Corps who holds medical and law degrees and served as deputy surgeon general during Trump’s first term.⁷⁸⁹

Trump also appointed Sean Slovenski, a former Walmart Health and Wellness senior vice president, as principal deputy director and chief operating officer, and Dr. Jennifer Shuford, formerly commissioner of the Texas Department of State Health Services, as deputy director and chief medical officer. Neither role requires Senate confirmation.¹⁰¹¹

Vaccine Policy Was Rewritten, Then Blocked in Court

In June 2025, Kennedy fired all 17 members of the Advisory Committee on Immunization Practices, the panel that makes national vaccine recommendations, and replaced them with 13 appointees who were known vaccine critics.¹²¹³¹⁴

Internal emails showed Kennedy also directed the CDC to pull flu vaccine advertising in February 2025 and shift toward “informed consent” messaging, forcing a pause of the agency’s “Wild to Mild” flu campaign. By mid-August 2025, a senior HHS aide had mandated “political review” of any major CDC policy decision by a Kennedy adviser.¹³

In March 2026, U.S. District Judge Brian Murphy in Boston blocked much of it. The court ruled that removing and replacing the ACIP members violated the Federal Advisory Committee Act’s “fair balance” and expertise requirements, and that the CDC had exceeded its statutory authority by unilaterally reducing the childhood immunization schedule without proper committee deliberation. The ruling invalidated the reconstituted panel’s votes and stayed 13 of Kennedy’s appointees.¹⁵ HHS filed a notice of appeal in American Academy of Pediatrics et al. v. Kennedy et al. on April 29, 2026.¹⁶

The 2025 Measles Outbreak

The vaccine fight ran alongside the worst measles outbreak in the United States in decades. By October 2025, more than 1,600 cases had been reported across 42 states, the highest count since 2000, and the outbreak ultimately caused more than 4,500 illnesses and at least 16 deaths across the U.S. and Mexico.¹⁷¹⁸

Between January and August 2025, the CDC posted only 10 times about measles on social media, and none of those posts encouraged MMR vaccination. When vaccines were mentioned at all, it was to describe outbreak response.¹⁷ Local health officials in Lubbock, Texas, struggled for weeks to get direct CDC support. Agency scientists did not reach out to local directors until after the first child in the Texas outbreak died on February 26, 2025; CDC teams did not arrive in Lubbock until March 7; and federal funding the state had requested did not arrive until May 21, 2025. Kennedy publicly promoted vitamin A as a treatment, and CDC scientists warned that pressure to include vitamin A in clinician communications led some parents to delay medical care.¹⁸

Restrictions on Publications, Data, and Communications

On January 21, 2025, federal health agencies were ordered to pause all external communications. The result was the first cancellation of the Morbidity and Mortality Weekly Report in its more than 60-year history: the January 23 and January 30 issues did not run, delaying three reports on avian influenza.¹⁹²⁰

Publication resumed February 6, 2025, but output dropped sharply. Between May and July 2025, MMWR published 35 articles compared to a historical average of 76 for that period. Every article now requires clearance from the HHS secretary’s office, and the CDC stopped sending embargoed content to reporters after March 2025. Some scientists stopped submitting work out of fear of political interference.¹⁹

On January 31, 2025, the CDC ordered scientists to retract or pause manuscripts containing terms the administration deemed forbidden, including “gender,” “transgender,” “LGBT,” and “non-binary,” to align with an executive order recognizing only two sexes.²¹ Collection of self-identified gender identity data was prohibited, and diversity, equity, and inclusion programs across the federal government were ended.²² All CDC documents became subject to executive branch review, and some staff were told they could not submit any new papers to outside journals regardless of topic, with much of the guidance delivered verbally.²³

Numerous datasets and webpages were removed, covering HIV/AIDS, hepatitis, tuberculosis, suicide, tobacco, pregnancy risks, and opioid-use disorder.²⁰ A February 2025 physicians’ lawsuit and a separate suit by the Washington State Medical Association resulted in a September 2025 settlement requiring HHS to restore more than 100 federal health websites and resources to their pre-removal state.²⁴

Workforce and Budget Cuts

The CDC has lost more than 25 percent of its workforce since fiscal year 2024, a net reduction of roughly 2,500 employees in fiscal 2025 and nearly 700 more in the first part of fiscal 2026.²⁵ The April 1, 2025, department-wide layoffs under the “Department of Government Efficiency Workforce Optimization Initiative” cut 10,000 HHS employees, 2,473 of them at the CDC.²⁶ In October 2025, dozens more were terminated in a single night, including approximately 70 Epidemic Intelligence Service disease detectives, the entire Washington office, and the staff of the MMWR.²⁷

Rehiring has lagged. HHS authorized roughly 900 new hires, but the CDC had made only 29 as of mid-2026. Employees said the agency was avoiding full-time hiring to sidestep priority-consideration requirements for laid-off staff. Critical leadership and subject-matter positions are being filled by rotating 120-day assignments, and about 96 CDC employees have been reclassified into “Schedule Policy/Career” status, an at-will designation that strips civil service protections. Half of respondents to a morale survey at the National Center for Emerging and Zoonotic Infectious Diseases described morale as “somewhat low” or “very low”; 4 percent called it “very high.”²⁵

Congress rejected the administration’s proposal to cut CDC funding by roughly 40 percent, appropriating $9.1 billion for fiscal 2026, a 0.2 percent decrease from the prior year.²⁸ In February 2026, the administration moved to cancel more than $600 million in CDC public health grants to California, Illinois, Colorado, and Minnesota. A federal judge in Illinois issued a temporary restraining order blocking the cuts, finding evidence they were driven by “hostility to what the federal government calls ‘sanctuary jurisdictions'” rather than legitimate agency priorities.²⁹

Global Health: The End of CDC’s PEPFAR Role

In May 2026, the State Department issued guidance effectively ending CDC involvement in the President’s Emergency Plan for AIDS Relief in most countries as of September 30, 2026. Under a new “America First Global Health Strategy,” PEPFAR funds will flow directly from the State Department to partner countries, which may then purchase CDC technical assistance at set fees.³⁰

PEPFAR, created in 2003 under George W. Bush, is credited with saving 26 million lives. The CDC had managed a substantial share of the program’s funding and maintained an on-the-ground presence in about 60 countries; the changes could close roughly one-third of those offices within three years.³¹ The administration froze PEPFAR payments earlier in Trump’s term as part of a broader foreign aid review; roughly 71 percent of USAID awards containing HIV activities were terminated, and analyses reported 71 percent of implementing partners had activity cancellations and 50 percent had staff cuts.³²

What Congress and the Courts Have Done

Pushback has come from both branches. House Appropriations Democrats held an April 2025 hearing on efforts to dismantle the CDC.³³ The Senate HELP Committee heard Kennedy testify in May 2025 on HHS restructuring, with Senator Bernie Sanders challenging him on terminated research grants and the measles outbreak.³⁴ In September 2025, Senate Permanent Subcommittee on Investigations minority staff issued a report identifying 57 instances of the administration undermining scientific institutions.²⁶ Congress also inserted legally binding funding details for nearly 60 budget accounts and new notification requirements for agencies terminating grants or contracts.²⁸

Federal courts have blocked the ACIP overhaul, forced restoration of removed health data, and paused the targeted grant cancellations. As of mid-2026, the CDC still has no Senate-confirmed director, Schwartz’s nomination is pending, and Bhattacharya continues performing the delegable duties of the office.³⁵ The American Medical Association has said the sustained turmoil “leaves us highly susceptible to public health threats.”⁴

1
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2
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